GC-MS analysis of diaminopimelic acid stereoisomers and amino acid enantiomers in rumen bacteria

Plasma d-amino acids are associated with markers of immune activation and organ dysfunction in people with HIV

BACKGROUND

d-Amino acids (d-AAs) have been associated with age-associated conditions in the general population but their relevance in people with HIV (PWH), who experience accentuated/accelerated aging has not been studied. We compared d-AA levels in HIV-infected and uninfected controls and explored their association with markers of immune activation, gut permeability and organ dysfunction.

DESIGN

Case-control analysis.

METHOD

Plasma samples from 60 antiretroviral therapy-treated HIV-infected individuals and 59 uninfected controls were analysed. A three-dimensional HPLC system was used to measure d-and l-asparagine, serine, alanine and proline and presented as %d-AA. Additionally, cell-associated and soluble markers of immune activation and senescence were characterized. Kidney and liver functions were expressed as estimated glomerular filtration rate and fibrosis-4 scores, respectively. Mann-Whitney and Spearman rank correlation coefficients were used for statistical analysis.

RESULTS

d-Asparagine, d-serine, d-alanine and d-proline were detectable in all plasma samples and correlated with age in HIV-infected and uninfected but not different between groups. Kynurenine/tryptophan ratio was positively correlated with all %d-AAs in PWH and with %d-serine and %d-proline in controls. %d-AAs were not consistently correlated with markers of gut permeability in both groups. All %d-AAs were also correlated with kidney function in both groups whereas age-associated accumulation of %d-asparagine, %d-serine and %d-proline were correlated with liver function and the VACS score in controls.

CONCLUSION

Plasma d-AAs are associated with chronological age and correlated with markers of immune activation and organ decline, though variably, in PWH and controls. Their role in the biology of aging warrants further investigation.

Determination of γ-D-glutamyl-meso-diaminopimelic acid in rumen fluid of dairy cows by pre-column chiral derivatization-HPLC

High concentrate (HC) diet feeding leads to the lysis of rumen microbes and the release of hazardous metabolites, which can trigger inflammatory responses, thereby impairing dairy cow health and production. γ-D-glutamyl-meso-diaminopimelic acid (iE-DAP), which constitutes the peptidoglycan (PGN) layer of bacteria, is the minimum PGN structure capable of activating inflammatory signaling pathways. This research paper aimed to determine the iE-DAP concentration and investigate the effects of an HC diet on the concentration of iE-DAP in the rumen fluid of dairy cows. However, there are limited studies on the determination of iE-DAP concentration. Hence, we established a high-performance liquid chromatography (HPLC) method combined with pre-column chiral derivatization to detect the concentration of iE-DAP in rumen fluid. Moreover, we conducted an animal experiment that included 12 lactating Holstein cows, which were randomly divided into a low-concentrate (LC) group and an HC group. The results showed that the linear range of iE-DAP was 5-500 µg/mL and that the intra- and inter-day RSDs were lower than 7%. Meanwhile, this method was successfully applied to the analysis of iE-DAP in rumen fluid, and the results revealed that long-term feeding with an HC diet elevated the concentration of iE-DAP in rumen fluid of dairy cows.

Stereospecificity control in aminoacyl-tRNA-synthetases: new evidence of d-amino acids activation and editing

The homochirality of amino acids is vital for the functioning of the translation apparatus. l-Amino acids predominate in proteins and d-amino acids usually represent diverse regulatory functional physiological roles in both pro- and eukaryotes. Aminoacyl-tRNA-synthetases (aaRSs) ensure activation of proteinogenic or nonproteinogenic amino acids and attach them to cognate or noncognate tRNAs. Although many editing mechanisms by aaRSs have been described, data about the protective role of aaRSs in d-amino acids incorporation remained unknown. Tyrosyl- and alanyl-tRNA-synthetases were represented as distinct members of this enzyme family. To study the potential to bind and edit noncognate substrates, Thermus thermophilus alanyl-tRNA-synthetase (AlaRS) and tyrosyl-tRNA-synthetase were investigated in the context of d-amino acids recognition. Here, we showed that d-alanine was effectively activated by AlaRS and d-Ala-tRNAAla, formed during the erroneous aminoacylation, was edited by AlaRS. On the other hand, it turned out that d-aminoacyl-tRNA-deacylase (DTD), which usually hydrolyzes d-aminoacyl-tRNAs, was inactive against d-Ala-tRNAAla. To support the finding about DTD, computational docking and molecular dynamics simulations were run. Overall, our work illustrates the novel function of the AlaRS editing domain in stereospecificity control during translation together with trans-editing factor DTD. Thus, we propose different evolutionary strategies for the maintenance of chiral selectivity during translation.

Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site

During protein synthesis, ribosomes discriminate chirality of amino acids and prevent incorporation of D-amino acids into nascent proteins by slowing down the rate of peptide bond formation. Despite this phenomenon being known for nearly forty years, no structures have ever been reported that would explain the poor reactivity of D-amino acids. Here we report a 3.7Å-resolution crystal structure of a bacterial ribosome in complex with a D-aminoacyl-tRNA analog bound to the A site. Although at this resolution we could not observe individual chemical groups, we could unambiguously define the positions of the D-amino acid side chain and the amino group based on chemical restraints. The structure reveals that similarly to L-amino acids, the D-amino acid binds the ribosome by inserting its side chain into the ribosomal A-site cleft. This binding mode does not allow optimal nucleophilic attack of the peptidyl-tRNA by the reactive α-amino group of a D-amino acid. Also, our structure suggests that the D-amino acid cannot participate in hydrogen-bonding with the P-site tRNA that is required for the efficient proton transfer during peptide bond formation. Overall, our work provides the first mechanistic insight into the ancient mechanism that helps living cells ensure the stereochemistry of protein synthesis.

Dissecting the mycobacterial cell envelope and defining the composition of the native mycomembrane

The mycobacterial envelope is unique, containing the so-called mycomembrane (MM) composed of very-long chain fatty acids, mycolic acids (MA). Presently, the molecular composition of the MM remains unproven, due to the diversity of methods used for determining its composition. The plasma membranes (PM) and the native MM-containing cell walls (MMCW) of two rapid-growing mycobacterial species, Mycobacterium aurum and M. smegmatis, were isolated from their cell lysates by differential ultracentrifugation. Transmission electron microscopy and biochemical analyses demonstrated that the two membranes were virtually pure. Bottom-up quantitative proteomics study indicated a different distribution of more than 2,100 proteins between the PM and MMCW. Among these, the mannosyltransferase PimB, galactofuranosyltransferase GlfT2, Cytochrome p450 and ABC transporter YjfF, were most abundant in the PM, which also contain lipoglycans, phospholipids, including phosphatidylinositol mannosides, and only a tiny amount of other glycolipids. Antigen85 complex proteins, porins and the putative transporters MCE protein family were mostly found in MMCW fraction that contains MA esterifying arabinogalactan, constituting the inner leaflet of MM. Glycolipids, phospholipids and lipoglycans, together with proteins, presumably composed the outer leaflet of the MM, a lipid composition that differs from that deduced from the widely used extraction method of mycobacterial cells with dioctylsulfosuccinate sodium.

Identification and elucidation of in vivo function of two alanine racemases from Pseudomonas putida KT2440

The genome of Pseudomonas putida KT2440 contains two open reading frames (ORFs), PP_3722 and PP_5269, that encode proteins with a Pyridoxal phosphate binding motif and a high similarity to alanine racemases. Alanine racemases play a key role in the biosynthesis of D-alanine, a crucial amino acid in the peptidoglycan layer. For these ORFs, we generated single and double mutants and found that inactivation of PP_5269 resulted in D-alanine auxotrophy, while inactivation of PP_3722 did not. Furthermore, as expected, the PP_3722/PP_5269 double mutant was a strict auxotroph for D-alanine. These results indicate that PP_5269 is an alr allele and that it is the essential alanine racemase in P. putida. We observed that the PP_5269 mutant grew very slowly, while the double PP_5269/PP_3722 mutant did not grow at all. This suggests that PP_3722 may replace PP_5269 in vivo. In fact, when the ORF encoding PP_3772 was cloned into a wide host range expression vector, ORF PP_3722 successfully complemented P. putida PP_5269 mutants. We purified both proteins to homogeneity and while they exhibit similar K_M values, the V_max of PP_5269 is fourfold higher than that of PP_3722. Here, we propose that PP_5269 and PP_3722 encode functional alanine racemases and that these genes be named alr-1 and alr-2 respectively.

D-Amino Acid Catabolism Is Common Among Soil-Dwelling Bacteria

Soil and rhizosphere environments were examined in order to determine the identity and relative abundance of bacteria that catabolize d- and l-amino acids as the sole source of carbon and nitrogen. All substrates were readily catabolized by bacteria from both environments, with most d-amino acids giving similar CFU counts to their l-amino acid counterparts. CFU count ratios between l- and d-amino acids typically ranged between 2 and 1. Isolates were phylogenetically typed in order to determine the identity of d-amino acid catabolizers. Actinobacteria, specifically the Arthrobacter genus, were abundant along with members of the α- and β-Proteobacteria classes.

Participation of D-serine in the development and reproduction of the silkworm Bombyx mori

The silkworm Bombyx mori contains high concentrations of free D-serine, an optical isomer of L-serine. To elucidate its function, we first investigated the localization of D-serine in various organs of silkworm larvae, pupae, and adult moths. Using immunohistochemical analysis with an anti-D-serine antibody, we found D-serine in the microvilli of midgut goblet and cylindrical cells and in peripheral matrix components of testicular and ovarian cells. By spectrophotometric analysis, D-serine was also found in the hemolymph and fat body. D-Alanine was not detected in the various organs by immunohistochemistry. Serine racemase, which catalyzes the inter-conversion of L- and D-serine, was found to co-localize with D-serine, and D-serine production from L-serine by intrinsic serine racemase was suggested. O-Phospho-L-serine is an inhibitor of serine racemase, and it was administered to the larvae to reduce the D-serine level. This reagent decreased the midgut caspase-3 level and caused a delay in spermatogenesis and oogenesis. The reagent also decreased mature sperm and egg numbers, suggesting D-serine participation in these processes. D-Serine administration induced an increase in pyruvate levels in testis, midgut, and fat body, indicating conversion of D-serine to pyruvate. On the basis of these results, together with our previous investigation of ATP biosynthesis in testis, we consider the possible involvement of D-serine in ATP synthesis for metamorphosis and reproduction.

Methemoglobin reduction mediated by D-amino acid dehydrogenase in Propsilocerus akamusi (Tokunaga) larvae

A methemoglobin (metHb) reduction system is required for aerobic respiration. In humans, Fe(III)-heme-bearing metHb (the oxidized form of hemoglobin), which cannot bind oxygen, is converted to Fe(II)-heme-bearing oxyhemoglobin (oxyHb, the reduced form), which can bind oxygen, in a system comprising NADH, NADH-cytochrome b5 reductase, and cytochrome b5. However, the mechanism of metHb reduction in organisms that inhabit oxygen-deficient environments is unknown. In the coelomic fluid of the larvae of Propsilocerus akamusi, which inhabit a microaerobic environment, we found that metHb was reduced by D-alanine. We purified an FAD-containing enzyme, D-amino acid dehydrogenase (DAD), and component V hemoglobin from the larvae. Using the purified components and spectrophotometric analyses, we showed a novel function of DAD: DAD-mediation of P. akamusi component V metHb reduction with using D-alanine as an electron donor. P. akamusi larvae possess this D-alanine-DAD metHb reduction system in addition to a previously discovered NADH-NADH-cytochrome b5 reductase system. This is the first report of the presence of DAD in a multicellular organism. The molecular mass of DAD was estimated to be 45 kDa. The optimal pH and temperature of the enzyme were 7.4 and 20 °C, respectively, and the optimal substrate was D-alanine. The enzyme activity was inhibited by benzoate and sulfhydryl-binding reagents.

Optimization and validation of a chiral GC-MS method for the determination of free D-amino acids ratio in human urine: application to a gestational diabetes mellitus study

Gestational Diabetes Mellitus (GDM) is defined as glucose intolerance with onset or first recognition during pregnancy. It is affecting approximately up to 14% of all pregnancies with an increasing tendency. GDM has been related to relevant short-term and long-term health complications for both mother and offspring. Recent studies strongly emphasized the role of several essential amino acids in the pathogenesis of obesity and highlighted their strong correlation with insulin resistance, but there are no references related to modifications in D-AAs in biological fluids. As D-AA elimination proceeds mainly by renal excretion, urine was the selected sample to evaluate the alterations in free D-AAs ratio in a GDM study. Only 1 mL of first void urine or standard solution was required for purification, by using a Discovery DSC-SCX SPE cartridge (500 mg/3 mL) and derivatization into their N(O)-pentafluoropropionyl amino acid 2-propyl esters. Enantiomeric separation was carried out by GC-MS on a Chirasil-L-Val N-propionyl-L-valine-tert-butylamide polysiloxane fused-silica capillary column (25 m×0.25 mm I.D., 0.12 μm film thickness, Agilent Technologies, Waldbronn, Germany), under programmed temperature elution. Detection was performed with an ion trap mass analyzer, operating in the full scan mode in the m/z 50-350 range. 14 pairs of derivatives of D-and L-AAs were separated. The steps of sample preparation, derivatization and GC-MS conditions were optimized for both urine and standards. Several conditions affecting the SPE procedure, such as sorbent mass/volume ratio of the cartridge, sample dilution and pH, were optimized. Volume of reagents and solvents and reaction temperature and time were also tested for the derivatization. Regarding the GC-MS parameters, split ratio, temperature program and mass range were optimized. The final method was validated in terms of linearity, sensitivity, accuracy and precision for D-Ala, D-Pro, D-Ser, D-Met, D-Phe, D-Glu, D-Orn and D-Lys. Identification of AAs in urine samples was based on retention time and mass spectra. Urine from 20 women with GDM and 20 pregnant women with normal glucose tolerance (after 2-h 75-g oral glucose tolerance test), matched according to the week of gestation and age (22-28 week of gestation and age 24-37 years), were enrolled into the study. %D-Relative amounts were determined for Ala, Val, Thr, Ser, Leu, Asx (Asp+Asn), Glx (Glu+Gln), Met, Phe, Tyr, Orn and Lys. Statistically significant differences (p<0.05) were observed only for D-Phe and higher values were found in the GDM group. It is possible that D-Phe could be involved in metabolic/signaling pathways to compensate early stages of insulin resistance, although further work is necessary to confirm this hypothesis.

Bacterial synthesis of D-amino acids

Recent work has shed light on the abundance and diversity of D-amino acids in bacterial extracellular/periplasmic molecules, bacterial cell culture, and bacteria-rich environments. Within the extracellular/periplasmic space, D-amino acids are necessary components of peptidoglycan, and disruption of their synthesis leads to cell death. As such, enzymes responsible for D-amino acid synthesis are promising targets for antibacterial compounds. Further, bacteria are shown to incorporate a diverse collection of D-amino acids into their peptidoglycan, and differences in D-amino acid incorporation may occur in response to differences in growth conditions. Certain D-amino acids can accumulate to millimolar levels in cell culture, and their synthesis is proposed to foretell movement from exponential growth phase into stationary phase. While enzymes responsible for synthesis of D-amino acids necessary for peptidoglycan (D-alanine and D-glutamate) have been characterized from a number of different bacteria, the D-amino acid synthesis enzymes characterized to date cannot account for the diversity of D-amino acids identified in bacteria or bacteria-rich environments. Free D-amino acids are synthesized by racemization or epimerization at the α-carbon of the corresponding L-amino acid by amino acid racemase or amino acid epimerase enzymes. Additionally, D-amino acids can be synthesized by stereospecific amination of α-ketoacids. Below, we review the roles of D-amino acids in bacterial physiology and biotechnology, and we describe the known mechanisms by which they are synthesized by bacteria.

Amino acids in the rhizosphere: from plants to microbes

Often referred to as the "building blocks of proteins", the 20 canonical proteinogenic amino acids are ubiquitous in biological systems as the functional units in proteins. Sometimes overlooked are their varying additional roles that include serving as metabolic intermediaries, playing structural roles in bioactive natural products, acting as cosubstrates in enzymatic transformations, and as key regulators of cellular physiology. Amino acids can also serve as biological sources of both carbon and nitrogen and are found in the rhizosphere as a result of lysis or cellular efflux from plants and microbes and proteolysis of existing peptides. While both plants and microbes apparently prefer to take up nitrogen in its inorganic form, their ability to take up and use amino acids may confer a selective advantage in certain environments where organic nitrogen is abundant. Further, certain amino acids (e.g., glutamate and proline) and their betaines (e.g., glycine betaine) serve as compatible solutes necessary for osmoregulation in plants and microbes and can undergo rapid cellular flux. This ability is of particular importance in an ecological niche such as the rhizosphere, which is prone to significant variations in solute concentrations. Amino acids are also shown to alter key phenotypes related to plant root growth and microbial colonization, symbiotic interactions, and pathogenesis in the rhizosphere. This review will focus on the sources, transport mechanisms, and potential roles of the 20 canonical proteinogenic amino acids in the rhizosphere.

Amino acid racemization in Pseudomonas putida KT2440

D-Amino acids have been shown to play an increasingly diverse role in bacterial physiology, yet much remains to be learned about their synthesis and catabolism. Here we used the model soil- and rhizosphere-dwelling organism Pseudomonas putida KT2440 to elaborate on the genomics and enzymology of d-amino acid metabolism. P. putida KT2440 catabolized the d-stereoisomers of lysine, phenylalanine, arginine, alanine, and hydroxyproline as the sole carbon and nitrogen sources. With the exception of phenylalanine, each of these amino acids was racemized by P. putida KT2440 enzymes. Three amino acid racemases were identified from a genomic screen, and the enzymes were further characterized in vitro. The putative biosynthetic alanine racemase Alr showed broad substrate specificity, exhibiting measurable racemase activity with 9 of the 19 chiral amino acids. Among these amino acids, activity was the highest with lysine, and the k(cat)/K(m) values with l- and d-lysine were 3 orders of magnitude greater than the k(cat)/K(m) values with l- and d-alanine. Conversely, the putative catabolic alanine racemase DadX showed narrow substrate specificity, clearly preferring only the alanine stereoisomers as the substrates. However, DadX did show 6- and 9-fold higher k(cat)/K(m) values than Alr with l- and d-alanine, respectively. The annotated proline racemase ProR of P. putida KT2440 showed negligible activity with either stereoisomer of the 19 chiral amino acids but exhibited strong epimerization activity with hydroxyproline as the substrate. Comparative genomic analysis revealed differences among pseudomonads with respect to alanine racemase genes that may point to different roles for these genes among closely related species.

Serine sublimes with spontaneous chiral amplification

Sublimation of near-racemic samples of serine yields a sublimate which is highly enriched in the major enantiomer; this simple one-step process occurs under relatively mild conditions, and represents a possible mechanism for the chiral amplification step in homochirogenesis.

Recent applications of stereoselective chromatography

Some recent applications of stereoselective chromatography in the fields of clinical pharmacy, drug analysis, food, and natural products are reviewed. The review is documented with up-to-date literature, which will assist further expansion of research in these areas.

Ascertainment of D-amino acids in germ-free, gnotobiotic and normal laboratory rats

Free D-amino acids were ascertained in the blood serum, urine and aqueous ethanolic extracts of feces of germ-free laboratory rats and a rat made gnotobiotic (tetra-associated) with species of Streptococcus, Lactobacillus and Clostridium. D-Amino acids were also determined in the brains of two germ-free rats. For comparison, D-amino acids were also measured in the blood serum of normal rats and the blood plasma, urine and feces of normal white mice. D-Enantiomers of most protein L-amino acids were detected in all physiological samples of animals. Quantities of free D-amino acids were determined as N(O)-pentafluoropropionyl-(2)-propyl esters by enantioselective gas chromatography and mass spectrometry. Stereoisomers of the bacterial marker 2,6-diaminopimelic acid, analyzed as N-trifluoroacetyl-(2)-propyl esters, were detected in feces of the gnotobiotic but not of the germ-free rat.

Determination of amino acid enantiomers in human urine and blood serum by gas chromatography-mass spectrometry

Amino acid (AA) enantiomers were determined as N(O)-pentafluoropropionyl-(2)-propyl esters by chiral gas chromatography-mass spectrometry (GC-MS) in 24 h samples of the urine of three healthy volunteers and in their blood sera. In urine the largest amounts were determined for D-Ser (64-199 micromol/day) and D-Ala (24-138 micromol/day). In blood sera, D-Ala (2.3-4.2 micromol/L) and D-Ser (1.0-2.9 micromol/L) were most abundant. Varying amounts of the D-enantiomers of Thr, Pro, Asx, Glx, Phe, Tyr, Orn and Lys were also found, albeit not in all urines and sera. Further, enantiomers were quantified in urine samples of two volunteers fasting for 115 h. Quantities of renally excreted D-AAs decreased in fasting, although amounts of D-Ser (69 and 77 micromol/L urine) as well as other D-AAs were still detectable. Time-dependent analyses of urine showed that D-AAs are continuously excreted.

Chromatographic determination of amino acid enantiomers in beers and raw materials used for their manufacture

Using gas chromatography (GC) on a chiral stationary phase, accompanied by high-performance liquid chromatography, beers and raw materials used for manufacturing (hops, barley grains, malts) were investigated for the pattern and quantities of amino acid enantiomers. Although L-amino acids were most abundant, certain D-amino acids were detected in all beers and most of the raw materials. Highest amounts of D-amino acids were detected in special beers such as Berliner Weisse that underwent bottle-conditioning with lactic cultures, and Belgian fruit beers produced by spontaneous fermentation. It is demonstrated that GC on chiral stationary phases is highly suitable for the quantitative determination of amino acid enantiomers in beers and raw materials used for their manufacture. Quantities, relative amounts and pattern of amino acid enantiomers can serve in particular as chiral markers for the authenticity of special beers.